Frequency Plot for aCGH
This analysis plots the copy number alteration frequencies for different groups. This analysis is performed on high-dimensional data nodes containing chromosomal region information.
This analysis represents a quick way to investigate alteration frequencies of the selected groups and is very similar to the advanced workflow analysis Group Test for aCGH, in which statistical testing is performed. It is advisable to use the Frequency Plot for aCGH analysis for exploratory purposes before performing statistical testing (which requires a significant amount of time).
To begin the analysis, see Running the Analyses, then perform the following steps.
To perform a Frequency Plot for aCGH analysis:
Click the Advanced Workflow tab, then open the Analysis menu.
Select Frequency Plot for aCGH.
The Variable Selection section appears.
Define the following variables:
- ArrayCGH: A high-dimensional data node containing the chromosomal regions.
- Group: Categorical data nodes separating the samples into two or more groups (though only one group may be plotted as well).
Click Run Analysis.
Frequency plots of copy number alterations in each defined group are shown. Frequencies of chromosomal gains are in blue and chromosomal losses are in red.
Example of a plot of one group:
- Mark A. van de Wiel, Kyung In Kim, Sjoerd J. Vosse, Wessel N. van Wieringen, Saskia M. Wilting and Bauke Ylstra. ” CGHcall: calling aberrations for array CGH tumor profiles.” Bioinformatics, 23, 892-894.